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crystal structure of porcine RNase 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RNF PDB ENTRY 1RNF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.1 M MORPHEUS BUFFER SYSTEM 3 PH 8.5, 0.12 M MONOSACCHARIDES, 30 % (V/V) EDO_P8K
Crystal Properties Matthews coefficient Solvent content 1.93 36.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.287 α = 90 b = 38.191 β = 97.68 c = 86.92 γ = 90
Symmetry Space Group I 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2013-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.25 43.07 99.9 0.06 15.9 6.6 32743 6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.27 100 0.39 4.4 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1RNF 1.25 43.07 31146 1596 99.84 0.12613 0.1248 0.1419 0.15272 0.1603 RANDOM 19.532
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.63 -0.05 -0.04 0.67
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.409 r_dihedral_angle_2_deg 31.709 r_dihedral_angle_4_deg 18.435 r_dihedral_angle_3_deg 12.882 r_sphericity_bonded 12.843 r_dihedral_angle_1_deg 7.281 r_scbond_it 3.313 r_rigid_bond_restr 2.687 r_mcangle_it 2.595 r_mcbond_it 2.053
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.409 r_dihedral_angle_2_deg 31.709 r_dihedral_angle_4_deg 18.435 r_dihedral_angle_3_deg 12.882 r_sphericity_bonded 12.843 r_dihedral_angle_1_deg 7.281 r_scbond_it 3.313 r_rigid_bond_restr 2.687 r_mcangle_it 2.595 r_mcbond_it 2.053 r_mcbond_other 2.051 r_angle_refined_deg 1.448 r_angle_other_deg 0.858 r_chiral_restr 0.095 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 979 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing